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10,609 Commits 63 Branches 243 Tags
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Commit Graph
5692 Commits
Author SHA1 Message Date
Carl Eberhard 59d539a321 Visualizations registry, QA: initial unit tests; Plugin framework unit tests: remove unneeded tests 2013-09-19 10:09:19 -04:00
Carl Eberhard d4a7c72bb5 Plugin frameworks, QA: add unit tests for PluginManager, HookPluginManager, and PageServingPluginManager 2013-09-18 18:24:00 -04:00
Carl Eberhard f131a96c46 Plugin framework: fix relative path parsing in PluginManager 2013-09-18 14:49:58 -04:00
Carl Eberhard 3a2cb607ac Plugin framework: factor out page serving responsibility, add HookPluginManager subclass and PageServingPluginManager subclass; Visualization registry: inherit from PageServingPluginManager 2013-09-18 10:53:12 -04:00
Dannon Baker 0ab2b1b023 Typo in toolshed util common. 2013-09-17 17:31:16 -04:00
Dannon Baker 692493ccba MetadataFile shouldn't attempt to create by default without checking exists() first. 2013-09-17 14:56:56 -04:00
Richard Burhans 29f96ebd3f Fix integrated_tool_panel dictionary before writing integrated_tool_panel.xml to keep tools/workflows in multiple sections 2013-09-17 14:37:36 -04:00
Kyle Ellrott 823634ab78 Adding way for API based tools job submissions to copy library dataset into history 2013-07-03 13:38:40 -07:00
Kyle Ellrott f0968770d6 The /api/tool submit can define inputs in the payload in the format {'id' : <encoded_id>, 'src' : 'hda'} 2013-06-27 15:52:08 -07:00
Kyle Ellrott 7cb0d9c6e4 Adding 'history' parameter to 'get_initial_value' method calls. This allows api based tool requests to build default parameters without having a fixed history attached to the 'trans' class 2013-06-27 14:23:12 -07:00
Carl Eberhard 29bc9a6a0f History API: add route/function to enable setting a current/working history; pack scripts 2013-09-12 14:06:21 -04:00
Daniel Blankenberg f2507abec5 Fix for unicode values in rst_to_html. 2013-09-12 10:55:16 -04:00
Dave Bouvier bcbdff9653 Fix for tool shed repository metadata API value mappers when time_last_tested is null for a metadata record. 2013-09-11 16:36:52 -04:00
James Taylor c9e4069f2c style: do not word wrap in pre blocks 2013-09-11 15:47:26 -04:00
Dave Bouvier 9649ffc5b0 Backward compatibility fix for installing repositories without repository dependencies. 2013-09-11 14:16:52 -04:00
Aysam Guerler be0f4bf6c8 Drag&drop multiple file upload, new js-based modal window and dynamic icon menu for master head 2013-09-11 11:25:00 -04:00
Dave Bouvier 948dac1d9f Fix for displaying repository dependencies that are not filtered out. 2013-09-10 16:35:48 -04:00
Dave Bouvier 19c8677bd9 Fix for filtering out repository dependencies that are only required when compiling a tool dependency because the precompiled binary was not found or failed to install. 2013-09-10 14:35:06 -04:00
Greg Von Kuster 75cb5f12fe Slight refactoring of message generation in the tool shed. 2013-09-10 14:19:46 -04:00
Greg Von Kuster 3adb3c6df7 Don't generate error messages when resetting metadata on installed tool shed repositories that have repository dependencies that are not installed because they were not needed for compiling the dependent repository's tool dependency. 2013-09-10 13:29:18 -04:00
Greg Von Kuster 61d81f7339 Framework enhancements for handling installation of repositories into Galaxy that have repository dependencies that are needed only for compiling a tool dependency. 2013-09-10 11:59:22 -04:00
Greg Von Kuster f82acbdeb9 Enable repository dependencies to be specially categorized if they should be installed only to allow the dependent repository's tool dependency to be compiled (in most cases the tool dependency should hopefully be installed as a compiled binary). 2013-09-09 14:26:58 -04:00
Martin Cech 17cb34ca0e reworked some jobs from the reports webapp and modified templates accordingly 
forces NO session for the DB because it is not needed
 2013-09-09 13:24:15 -04:00
Richard Burhans f3e2b48453 Fixed initial installation of virtualenv 2013-09-06 18:03:51 -04:00
Dave Bouvier 354930e549 Fix tool shed API value mappers. 2013-09-06 17:06:18 -04:00
Greg Von Kuster 3af26a17b0 Partial framework support for enhanced tool dependency definitions that enable installation of binaries into specified architectures. More coming soon... 2013-09-06 09:38:12 -04:00
Nate Coraor 3d69348ff1 Add the now-required 'config' param to the DistributedObjectStore's call to the superclass __jnit__(). 2013-09-05 15:28:44 -04:00
Jeremy Goecks 1cfb5be961 Correctly treat VCF format and genotyping fields as optional. 2013-09-05 14:19:50 -04:00
Dave Bouvier 0d8f353fca Merge in bugfix from stable. 2013-09-04 14:34:57 -04:00
Dave Bouvier 5e4ec92712 Fix for duplicate records created when a repository is installed from the tool shed, and the same repository had previously been installed and uninstalled. 2013-09-04 14:30:49 -04:00
Dave Bouvier 8d1b7cab70 Tool dependency definitions: Add <actions_group> tag and support for filtering contained <actions> tags by architecture and operating system. 2013-09-03 12:22:29 -04:00
Greg Von Kuster 4fcf06c995 Convert markupsafe object to unicode before rendering in the tool shed. 2013-09-03 11:10:50 -04:00
Greg Von Kuster 402c469973 Fix for rendering various files in the tool shed. Specific files should now correctly and safely render as html or rst. 2013-09-03 10:44:53 -04:00
Jeremy Goecks a747bf1615 Remove unneeded to_dict code/methods. 2013-08-30 14:23:42 -04:00
Jeremy Goecks 7421a130fd DictifiableMixin cleanup: (a) remove 'Mixin' from name and (b) rename dictify to to_dict. 2013-08-30 14:17:23 -04:00
Jeremy Goecks efaf9936c9 Use super() to call dictify() rather than calling directly. 2013-08-30 14:09:18 -04:00
Greg Von Kuster bf48030e2a Fix for zero-based comparison in the tool shed. 2013-08-30 13:08:22 -04:00
Dannon Baker 42148d4187 Re-apply changes that got reverted in 10492:8f6f926f912e 2013-08-30 12:06:10 -04:00
Greg Von Kuster 23233df329 Enhance the update_available feature for installed tool shed repositories to enable any type of status from the tool shed for each repository. The Installed tool shed repositories grid now displays whether there are revision updates available, revision upgrades available, whether the revision is the latest installable revision, and whether the repository has been deprecated in the tool shed. This change set includes a 0016 db table migration script for which it has been discovered that it is no longer possible to drop a column from a database table using a migration script if the database is sqlite. 2013-08-30 11:47:27 -04:00
Dannon Baker 0f120bd92c Strip trailing whitespace (and windows line endings) from all python files in lib 2013-08-29 23:39:52 -04:00
Dannon Baker b6ffddd02b Strip trailing whitespace in data_providers 2013-08-29 23:32:37 -04:00
Dannon Baker 916deeb5dd Realizing it's abstract, still require appropriate inputs to get_data in BaseDataProvider 2013-08-29 23:31:55 -04:00
Dannon Baker 1bb35fa113 Data manager element loading assertion would fail if executed; use elem.tag and not root.tag 2013-08-29 23:26:57 -04:00
Dannon Baker 68c6bdf0f4 Add missing os import to ngsindex.py 2013-08-29 23:24:24 -04:00
Dannon Baker c8631a10a0 Variable confusion in dataproviders/dataset -- clarify and use correct indices var 2013-08-29 23:20:05 -04:00
Dannon Baker 275622c6d7 dataprovider dataset cleanup, add missing bx.bbi import 2013-08-29 23:17:36 -04:00
Dannon Baker f18e3ca831 Strip unused imports (and trailing whitespace) from genome data provider 2013-08-29 23:14:17 -04:00
Dannon Baker 30565dc959 Add missing import parse_gff_attributes to genome data provider 2013-08-29 23:10:02 -04:00
Dannon Baker 8a957a5449 Explicitly require source argument to RawBedDataProvider.get_iterator instead of relying on it in kwargs 2013-08-29 23:06:53 -04:00
Dannon Baker 46127b2bf5 Add missing os import to cli_shell/rsh 2013-08-29 23:00:04 -04:00